Jihan Yehia

Publication Date

Fall 2023

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)


Computer Science

First Advisor

Wendy Lee

Second Advisor

William Andreopoulos

Third Advisor

Philip Heller


walnut extract (WE), triple negative breast cancer (TNBC), specificity protein 1 (Sp1), RNA-seq pipeline, differential gene expression (DGE), Illumina, Nanopore


Walnut extract (WE) has shown promising anti-cancer effects, such as inducing apoptosis and moderating cell cycle progression. A previous study by Dr. Brandon White’s Lab at San Jose State University hypothesizes that WE can downregulate the expression of the pro-tumoral specificity protein 1 (Sp1) in triple negative breast cancer (TNBC). This project builds an RNA-seq pipeline that runs differential gene expression (DGE) analysis to study the effect of WE on TNBC, thereby offering a wider perspective on genes that may be affected by this treatment. The data used in this project originated from Illumina and Nanopore sequencing methods, and DGE analysis was run on both datasets to evaluate their efficiency and accuracy. The RNA-seq analysis identified differentially expressed genes and pathways in response to WE. Some of these pathways corroborated with the anti-cancer effects of WE, while others did not. Further investigations should be conducted to validate the obtained results.